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Volumn 55, Issue 3, 2004, Pages 519-528

Protein Secondary Structure Assignment Through Voronoï Tessellation

Author keywords

helices; strands; Contact matrices; Vorono tessellation

Indexed keywords

AMINO ACID ANALYSIS; ARTICLE; AUTOMATION; GEOMETRY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; RESIDUE ANALYSIS; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; VORONOI TESSELLATION ASSIGNMENT PROCEDURE;

EID: 2442596233     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10566     Document Type: Article
Times cited : (54)

References (50)
  • 1
    • 76549252207 scopus 로고
    • The structure of proteins: Two hydrogen-bonded helical configurations of the polypetptide chain
    • Pauling L, Corey RB, Branson HR. The structure of proteins: two hydrogen-bonded helical configurations of the polypetptide chain. Proc Natl Acad Sci USA 1951;37:205-234.
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 205-234
    • Pauling, L.1    Corey, R.B.2    Branson, H.R.3
  • 2
    • 0000573263 scopus 로고
    • Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets
    • Pauling L, Corey RB. Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc Natl Acad Sci USA 1951;37:729-740.
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 729-740
    • Pauling, L.1    Corey, R.B.2
  • 3
    • 0015114095 scopus 로고
    • Folding of polypeptide chains in proteins: A proposed mechanism for folding
    • Lewis PN, Momany FA, Scheraga HA. Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc Natl Acad Sci USA 1971;68:2293-2297.
    • (1971) Proc Natl Acad Sci USA , vol.68 , pp. 2293-2297
    • Lewis, P.N.1    Momany, F.A.2    Scheraga, H.A.3
  • 4
    • 0015530828 scopus 로고
    • Protein folding
    • Kuntz ID. Protein folding. J Am Chem Soc 1972;94:4009-4012.
    • (1972) J Am Chem Soc , vol.94 , pp. 4009-4012
    • Kuntz, I.D.1
  • 6
    • 0017701604 scopus 로고
    • Automatic identification of secondary structure in globular proteins
    • Levitt M, Greer J. Automatic identification of secondary structure in globular proteins. J Mol Biol 1977;114:181-239.
    • (1977) J Mol Biol , vol.114 , pp. 181-239
    • Levitt, M.1    Greer, J.2
  • 7
    • 0017388774 scopus 로고
    • A new algorithm for finding the peptide chain turns in a globular protein
    • Rose GD, Seltzer JP. A new algorithm for finding the peptide chain turns in a globular protein. J Mol Biol 1977;113:153-164.
    • (1977) J Mol Biol , vol.113 , pp. 153-164
    • Rose, G.D.1    Seltzer, J.P.2
  • 8
    • 0017709445 scopus 로고
    • Beta-turns in proteins
    • Chou PY, Fasman GD. Beta-turns in proteins. J Mol Biol 1977;115: 135-175.
    • (1977) J Mol Biol , vol.115 , pp. 135-175
    • Chou, P.Y.1    Fasman, G.D.2
  • 10
    • 0020186244 scopus 로고
    • Identification of secondary structures in globular proteins - A new algorithm
    • Ramakrishnan C, Soman KV. Identification of secondary structures in globular proteins-a new algorithm. Int J Pept Protein Res 1982;20:218-237.
    • (1982) Int J Pept Protein Res , vol.20 , pp. 218-237
    • Ramakrishnan, C.1    Soman, K.V.2
  • 11
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 12
    • 0023927904 scopus 로고
    • Identification of structural motifs from protein coordinate data: Secondary structure and first-level super-secondary structure
    • Richards FM, Kundrot CE. Identification of structural motifs from protein coordinate data: secondary structure and first-level super-secondary structure. Proteins 1988;3:71-84.
    • (1988) Proteins , vol.3 , pp. 71-84
    • Richards, F.M.1    Kundrot, C.E.2
  • 13
    • 0024821134 scopus 로고
    • Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis
    • Sklenar H, Etchebest C, Lavery R. Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 1989;6:46-60.
    • (1989) Proteins , vol.6 , pp. 46-60
    • Sklenar, H.1    Etchebest, C.2    Lavery, R.3
  • 14
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 15
    • 0027207221 scopus 로고
    • Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment
    • Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP. Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng 1993;6:377-382.
    • (1993) Protein Eng , vol.6 , pp. 377-382
    • Colloc'h, N.1    Etchebest, C.2    Thoreau, E.3    Henrissat, B.4    Mornon, J.P.5
  • 16
    • 0030998184 scopus 로고    scopus 로고
    • P-SEA: A new efficient assignment of secondary structure from C α trace of proteins
    • Labesse O, Colloc'h N, Pothier J, Mornon JP. P-SEA: a new efficient assignment of secondary structure from C α trace of proteins. Comput Appl Biosci 1997;13:291-295.
    • (1997) Comput Appl Biosci , vol.13 , pp. 291-295
    • Labesse, O.1    Colloc'h, N.2    Pothier, J.3    Mornon, J.P.4
  • 17
    • 84927514013 scopus 로고
    • Recherches sur les paralleloedres primitifs
    • Voronoï G. Recherches sur les paralleloedres primitifs. J Reine Angew Math 1908;134:198-287.
    • (1908) J Reine Angew Math , vol.134 , pp. 198-287
    • Voronoï, G.1
  • 18
    • 0016816308 scopus 로고
    • Volume occupation, environment and accessibility in proteins. The problem of the protein surface
    • Finney JL. Volume occupation, environment and accessibility in proteins. The problem of the protein surface. J Mol Biol 1975;96: 721-732.
    • (1975) J Mol Biol , vol.96 , pp. 721-732
    • Finney, J.L.1
  • 19
    • 0034778102 scopus 로고    scopus 로고
    • Determining the minimum number of types necessary to represent the sizes of protein atoms
    • Tsai J, Voss N, Gerstein M. Determining the minimum number of types necessary to represent the sizes of protein atoms. Bioinformatics 2001;17:949-956.
    • (2001) Bioinformatics , vol.17 , pp. 949-956
    • Tsai, J.1    Voss, N.2    Gerstein, M.3
  • 21
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 22
    • 0029790358 scopus 로고    scopus 로고
    • Packing at the protein-water interface
    • Gerstein M, Chothia C. Packing at the protein-water interface. Proc Natl Acad Sci USA 1996;93:10167-10172.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 10167-10172
    • Gerstein, M.1    Chothia, C.2
  • 23
    • 0015977588 scopus 로고
    • The interpretation of protein structures: Total volume, group volume distributions and packing density
    • Richards FM. The interpretation of protein structures: total volume, group volume distributions and packing density. J Mol Biol 1974;82:1-14.
    • (1974) J Mol Biol , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 24
    • 0031853406 scopus 로고    scopus 로고
    • New scoring schemes for protein fold recognition based on Voronoi contacts
    • Zimmer R, Wohler M, Thiele R. New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinformatics 1998;14: 295-308.
    • (1998) Bioinformatics , vol.14 , pp. 295-308
    • Zimmer, R.1    Wohler, M.2    Thiele, R.3
  • 25
    • 0031310710 scopus 로고    scopus 로고
    • A new approach to protein fold recognition based on Delaunay tessellation of protein structure
    • Zheng W, Cho SJ, Vaisman II, Tropsha A. A new approach to protein fold recognition based on Delaunay tessellation of protein structure. Pac Symp Biocomput 1997;486-497.
    • (1997) Pac Symp Biocomput , pp. 486-497
    • Zheng, W.1    Cho, S.J.2    Vaisman, I.I.3    Tropsha, A.4
  • 26
    • 0030806961 scopus 로고    scopus 로고
    • Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
    • Munson PJ, Singh RK. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 1997;6: 1467-1481.
    • (1997) Protein Sci , vol.6 , pp. 1467-1481
    • Munson, P.J.1    Singh, R.K.2
  • 27
    • 0030054951 scopus 로고    scopus 로고
    • Delaunay tessellation of proteins: Four body nearest-neighbor propensities of amino acid residues
    • Singh RK, Tropsha A, Vaisman, II. Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J Comput Biol 1996;3:213-221.
    • (1996) J Comput Biol , vol.3 , pp. 213-221
    • Singh, R.K.1    Tropsha, A.2    Vaisman, I.I.3
  • 28
    • 0031736346 scopus 로고    scopus 로고
    • Novel method to detect a motif of local structures in different protein conformations
    • Wako H, Yamato T. Novel method to detect a motif of local structures in different protein conformations. Protein Eng 1998;11: 981-990.
    • (1998) Protein Eng , vol.11 , pp. 981-990
    • Wako, H.1    Yamato, T.2
  • 29
    • 0036892439 scopus 로고    scopus 로고
    • Nonatomic solvent-driven Voronoi tessellation of proteins: An open tool to analyze protein folds
    • Angelov B, Sadoc JF, Jullien R, Soyer A, Mornon JP, Chomilier J. Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds. Proteins 2002;49:446-456.
    • (2002) Proteins , vol.49 , pp. 446-456
    • Angelov, B.1    Sadoc, J.F.2    Jullien, R.3    Soyer, A.4    Mornon, J.P.5    Chomilier, J.6
  • 30
    • 0034287449 scopus 로고    scopus 로고
    • Voronoi tessellation reveals the condensed matter character of folded proteins
    • Soyer A, Chomilier J, Mornon JP, Jullien R, Sadoc JF. Voronoi tessellation reveals the condensed matter character of folded proteins. Phys Rev Lett 2000;85:3532-3535.
    • (2000) Phys Rev Lett , vol.85 , pp. 3532-3535
    • Soyer, A.1    Chomilier, J.2    Mornon, J.P.3    Jullien, R.4    Sadoc, J.F.5
  • 31
    • 0014898597 scopus 로고
    • The development of crystallographic enzymology
    • Phillips DC. The development of crystallographic enzymology. Biochem Soc Symp 1970;30:11-28.
    • (1970) Biochem Soc Symp , vol.30 , pp. 11-28
    • Phillips, D.C.1
  • 32
    • 0015949278 scopus 로고
    • Comparison of homologous tertiary structures of proteins
    • Nishikawa K, Ooi T. Comparison of homologous tertiary structures of proteins. J Theor Biol 1974;43:351-374.
    • (1974) J Theor Biol , vol.43 , pp. 351-374
    • Nishikawa, K.1    Ooi, T.2
  • 33
    • 0036763251 scopus 로고    scopus 로고
    • Prediction of protein residue contacts with a PDB-derived likelihood matrix
    • Singer MS, Vriend G, Bywater RP. Prediction of protein residue contacts with a PDB-derived likelihood matrix. Protein Eng 2002;15:721-725.
    • (2002) Protein Eng , vol.15 , pp. 721-725
    • Singer, M.S.1    Vriend, G.2    Bywater, R.P.3
  • 34
    • 0028984809 scopus 로고
    • Contact pattern-induced pair potentials for protein fold recognition
    • Selbig J. Contact pattern-induced pair potentials for protein fold recognition. Protein Eng 1995;8:339-351.
    • (1995) Protein Eng , vol.8 , pp. 339-351
    • Selbig, J.1
  • 35
    • 0019860994 scopus 로고
    • Correlation of DNA exonic regions with protein structural units in haemoglobin
    • Go M. Correlation of DNA exonic regions with protein structural units in haemoglobin. Nature 1981;291:90-92.
    • (1981) Nature , vol.291 , pp. 90-92
    • Go, M.1
  • 36
    • 0034870539 scopus 로고    scopus 로고
    • Ab initio modeling of small, medium, and large loops in proteins
    • Galaktionov S, Nikiforovich GV, Marshall GR. Ab initio modeling of small, medium, and large loops in proteins. Biopolymers 2001;60:153-168.
    • (2001) Biopolymers , vol.60 , pp. 153-168
    • Galaktionov, S.1    Nikiforovich, G.V.2    Marshall, G.R.3
  • 37
    • 0036708474 scopus 로고    scopus 로고
    • Efficient generation of feasible pathways for protein conformational transitions
    • Kim MK, Jernigan RL, Chirikjian GS. Efficient generation of feasible pathways for protein conformational transitions. Biophys J 2002;83:1620-1630.
    • (2002) Biophys J , vol.83 , pp. 1620-1630
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 38
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 40
    • 0029199404 scopus 로고
    • Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 2. Structure of beta-purothionin at 1.7 Å resolution
    • Stec B, Rao U, Teeter MM. Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 2. Structure of beta-purothionin at 1.7 Å resolution. Acta Crystallogr D Biol Crystallogr 1995;51:914-924.
    • (1995) Acta Crystallogr D Biol Crystallogr , vol.51 , pp. 914-924
    • Stec, B.1    Rao, U.2    Teeter, M.M.3
  • 42
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 43
    • 0032528935 scopus 로고    scopus 로고
    • Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: The role of Glu88 in the unique substrate-recognition mechanism
    • Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K. Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism. Structure 1998;6:971-982.
    • (1998) Structure , vol.6 , pp. 971-982
    • Imada, K.1    Inagaki, K.2    Matsunami, H.3    Kawaguchi, H.4    Tanaka, H.5    Tanaka, N.6    Namba, K.7
  • 44
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF-a program to identify and analyze structural motifs in proteins
    • Hutchinson EG, Thornton JM. PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci 1996;5: 212-220.
    • (1996) Protein Sci , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 45
    • 0030040589 scopus 로고    scopus 로고
    • Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58
    • Parkin S, Rupp B, Hope H. Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58. Acta Crystallogr D Biol Crystallogr 1996;52:18-29.
    • (1996) Acta Crystallogr D Biol Crystallogr , vol.52 , pp. 18-29
    • Parkin, S.1    Rupp, B.2    Hope, H.3
  • 46
    • 0025767350 scopus 로고
    • Beta-breakers: An aperiodic secondary structure
    • Colloc'h N, Cohen FE. Beta-breakers: an aperiodic secondary structure. J Mol Biol 1991;221:603-613.
    • (1991) J Mol Biol , vol.221 , pp. 603-613
    • Colloc'h, N.1    Cohen, F.E.2
  • 47
    • 0026596926 scopus 로고
    • A segment-based approach to protein secondary structure prediction
    • Presnell SR, Cohen BI, Cohen FE. A segment-based approach to protein secondary structure prediction. Biochemistry 1992;31:983-993.
    • (1992) Biochemistry , vol.31 , pp. 983-993
    • Presnell, S.R.1    Cohen, B.I.2    Cohen, F.E.3
  • 48
    • 0030585429 scopus 로고    scopus 로고
    • Crystal structures of reduced, oxidized, and mutated human thioredoxins: Evidence for a regulatory homodimer
    • Weichsel A, Gasdaska JR, Powis G, Montfort WR. Crystal structures of reduced, oxidized, and mutated human thioredoxins: evidence for a regulatory homodimer. Structure 1996;4:735-751.
    • (1996) Structure , vol.4 , pp. 735-751
    • Weichsel, A.1    Gasdaska, J.R.2    Powis, G.3    Montfort, W.R.4
  • 49
    • 0030067454 scopus 로고    scopus 로고
    • Refinement and structural analysis of bovine cytochrome B(5) at 1.5 angstrom resolution
    • Durley RCE, Mathews FS. Refinement and structural analysis of bovine cytochrome B(5) at 1.5 angstrom resolution. Acta Crystallogr D Biol Crystallogr 1996;52:65-76.
    • (1996) Acta Crystallogr D Biol Crystallogr , vol.52 , pp. 65-76
    • Durley, R.C.E.1    Mathews, F.S.2


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